cleaning up a bit

ChemID.py

@@ -17,13 +17,15 @@ from rdkit.Chem import Descriptors,Descriptors3D, Draw
 def ResolveChemical(chemName, IDtype):
 
     if IDtype == 'CAS':
-        smiles = cas2smiles(chemName)
+        cas = chemName
+        smiles = cas2smiles(cas)
+        name = cas2name(cas)
         mol = Chem.MolFromSmiles(smiles)
         Mw = Descriptors.MolWt(mol)
         im = ImageFromSmiles(smiles)
         im64 = Imageto64(im)
 
-    return (smiles, Mw, mol, im64)
+    return (name, cas, smiles, Mw, im64)
 
 #Generates an image of the molecule represented by the SMILES code given.
 #Returns None if the image cannot be generated. From https://github.com/ronaldo-prata/flask-test/blob/master/functions.py
@@ -43,14 +45,8 @@ def ImageFromSmiles(smiles):
 
 def wTrim(img):
     bbox = ImageOps.invert(img).getbbox()
-
     crop = (bbox[0], bbox[1], bbox[2], bbox[3])
-    # if (bbox[2]-bbox[0] < 100 and bbox[3]-bbox[1] < 100):
-    #     crop = (300, 300, 700, 700)
-    # elif (bbox[2]-bbox[0] > bbox[3]-bbox[1]):
-    #     crop = (bbox[0], bbox[0], bbox[2], bbox[2])
-    # else:
-    #     crop = (bbox[1], bbox[1], bbox[3], bbox[3])
+
     return img.crop(crop)
 
 #Converts a PIL image into its base64 representation.
@@ -102,6 +98,39 @@ def cas2smiles(cas):
             smiles = None
     return smiles
 
+# function to convert cas to name
+def cas2name(cas):
+    name = None
+    #if not is_cas(cas):
+    #    name = 'INVALID CAS'
+    # first try chemicals package
+    if not name:
+        try:
+            cm = chemicals.search_chemical(cas)
+            name = cm.common_name
+        except:
+            name = None
+    # then try cirpy
+    if not name:
+        try:
+            name = cirpy.resolve(cas, 'iupac_name')
+        except:
+            name = None
+    if type(name) is list:
+        name = name[0]
+    # next try pubchem for compounds
+    if not name:
+        try:
+            compounds = pcp.get_compounds(cas, namespace='name')
+            c = compounds[0]
+            name = c.iupac_name
+            if not name:
+                # have seen empty iupac_name before, try synonyms if this happens
+                name = c.synonyms[0]
+        except:
+            name = None
+    return name
+
 # function to convert chemical entity string to iupac name
 def string2name(string):
     name = None

exposure_module/exposure.py

@@ -21,7 +21,7 @@ def exp_post():
     chemName = request.form["chemName"]
     IDtype = request.form["IDtype"]
 
-    smiles, MW, mol, molImage = ResolveChemical(chemName, IDtype)
+    iupac, cas, smiles, MW, molImage = ResolveChemical(chemName, IDtype)
 
     amount = float(request.form["amount"])
     mass = float(request.form["mass"])
@@ -67,4 +67,4 @@ def exp_post():
 
     return render_template('exposure_report.html', polymers=polymers, pIndex=pIndex, release=release,
                            assume=assume, area=area, vol=vol, amount=amount, diff=diff, time=time, exposure=exposure, TTC=TTC,
-                           MOS=MOS, chemName=chemName, image=pngImageB64String, MW=MW, smiles=smiles, molImage=molImage)
+                           MOS=MOS, chemName=chemName, image=pngImageB64String, MW=MW, iupac=iupac, cas=cas, smiles=smiles, molImage=molImage)

exposure_module/templates/exposure_index.html

@@ -36,14 +36,13 @@ For details on how to use CHRIS, please click the information icons next to each
 
   Identifier type: <select name="IDtype">
     <option value="CAS" selected>CAS</option>
-    <option value="IUPAC" >IUPAC</option>
     <option value="SMILES" >SMILES</option>
     <option value="common" >Common name</option>
   </select> <br>
 
   Identifier: <input name="chemName" id="chemName" type="text" value="" required><br>
 
-  Amount (mg): <input name="amount" id="amount" value="1.0" step="any" min="0.000001" type="number"> <br>
+  Amount (mg): <input name="amount" id="amount" value="1.0" step="any" min="0.000001" type="number" required> <br>
 
   <!-- Modal -->
   <div id="LeachModal" class="modal fade" role="dialog">
@@ -78,8 +77,8 @@ Matrix: <select name="polymer">
     <option value="{{polymer}}">{{polymer}}</option>
   {% endfor %}
 </select> <br>
-Mass (g): <input name="mass" id="mass" step="any" value="1.0" min="0.000001" type="number"> <br>
-Density (g/cm<sup>3</sup>): <input name="density" id="density" step="any" value="1.0" min="0.01" type="number">
+Mass (g): <input name="mass" id="mass" step="any" value="1.0" min="0.000001" type="number" required> <br>
+Density (g/cm<sup>3</sup>): <input name="density" id="density" step="any" value="1.0" min="0.01" type="number" required>
 
 <!-- Modal -->
 <div id="PolymerModal" class="modal fade" role="dialog">
@@ -108,13 +107,13 @@ Density (g/cm<sup>3</sup>): <input name="density" id="density" step="any" value=
 
   <h3> Device characteristics <button type=button class="Info_btn" data-toggle="modal" data-target="#DeviceModal">&#9432;</button> </h3>
   Exposed surface area (cm<sup>2</sup>):
-  <input name="area" id="area" step="any" value="5.0" min="0.001" type="number"><br>
+  <input name="area" id="area" step="any" value="5.0" min="0.001" type="number" required><br>
   Exposure type:
   <input type="radio" name="exposure" id="long-term" value="long-term" onclick="javascript:exposureCheck();" checked > long-term
   <input type="radio" name="exposure" id="prolonged" value="prolonged" onclick="javascript:exposureCheck();" > prolonged
   <input type="radio" name="exposure" id="limited" value="limited" onclick="javascript:exposureCheck();" > limited
   <span id="limitedtime" style="visibility:hidden">
-    &nbsp; &rArr; Exposure time (h): <input name="exptime" id="time" step="any" min="0.001" max="24" value="24" type="number" ><br>
+    &nbsp; &rArr; Exposure time (h): <input name="exptime" id="time" step="any" min="0.001" max="24" value="24" type="number" required><br>
   </span>
 
 <!-- Modal -->

exposure_module/templates/exposure_report.html

@@ -50,9 +50,10 @@
 <div class="container">
 <div class="row">
   <div class="column">
-      Name =  <br> <br>
-      Molecular weight = {{MW}} <br> <br>
-      SMILES = {{smiles}}
+      IUPAC Name ::  {{iupac}} <br> <br>
+      CAS ::  {{cas}} <br> <br>
+      Molecular weight :: {{MW}} <br> <br>
+      SMILES :: {{smiles}}
   </div>
   <div class="column">
       <img src="{{molImage}}"/>